The Prime Minister has been warned that failing to fully deliver the Northern Powerhouse Rail (NPR) high speed scheme would be a "hammer blow" for the region in its efforts to recover from the pandemic.
The Yorkshire Post has seen government documents which suggest that rather than building a new high speed rail line between Leeds and Manchester, the project could now follow the route of the existing Trans-Pennine line through Huddersfield and Dewsbury.
The Treasury is this week set to consider plans to massively increase the budget for the Transpennine Route Upgrade (TRU) in a move that would cut journey times and improve reliability.
But northern leaders fear that by developing NPR alongside TRU it could mean the high speed rail route would not include a station in Bradford city centre, something considered vital for the city's economic fortunes.
Under previous Transport Secretary Chris Grayling, the TRU scheme was valued at £2.9bn but the documents say the total cost is now between £9bn and £11.5bn.
The plans would see journeys from Manchester to Leeds fall from 49 minutes to 40 minutes and Manchester to York from 74 to 62 minutes. And the number of trains between Leeds and Manchester would increase from six per hour to eight.
Officials say the investment would cut the number of minutes lost to delays in half and create 15 new opportunities for freight per day.
This proposal would include full electrification all the way from Manchester to Colton Junction, south of York, something which the document says would contribute "strongly to 'net zero' carbon reduction obligations".
Among the key elements of investment in the next two years are what are described as "development of capacity improvements for NPR between Ravensthorpe and Dewsbury".
This includes four tracks on the line between Cross Gates and Garforth east of Leeds and three tracks between Marsden and Huddersfield, on the existing route of the Transpennine Route.
But the move has prompted fears at Transport for the North, the body which represents northern leaders, that the Government will ignore their pleas for an entirely new line between Leeds and Manchester serving Bradford city centre.
Last year TfN said its preferred route for NPR was a Bradford 'gateway' option which would cut the time to travel between Leeds and Manchester to 26 minutes and 30 seconds and provide a huge boost to the economy of a city which has long been let down by its poor transport links.
But Department for Transport officials have also discussed a £4bn cheaper 'Diggle' option which largely follows the existing Transpennine route through Huddersfield and does not serve Bradford at all.
In a speech in 2019, Boris Johnson said he wanted "to be the Prime Minister who does with Northern Powerhouse Rail what we did for Crossrail in London". He said: "And today I am going to deliver on my commitment to that vision with a pledge to fund the Leeds to Manchester route."
Bradford council leader Susan Hinchcliffe said: "As the youngest city in the UK, Bradford is at the heart of the future workforce of the North. Young people have been hugely impacted by the economic restrictions of the pandemic.
"Government should not take a decision now therefore which will doubly disadvantage these young people for the rest of their lives.
"Transpennine upgrade needs to happen but it should be in addition to, not instead of having Bradford city central as a stop on the mainline NPR."
West Yorkshire mayor Tracy Brabin said: “I have contacted the Transport Secretary to seek urgent clarity around this matter.
“Bradford is a city with great potential and opportunity, but if we are to see this fantastic place grow and prosper then it needs the NPR new line going through it with a new major station for Bradford. How can it be right that the 6th biggest city in the UK does not have an adequate rail service?
“We have been consistently clear that we need a transport system that works for people who live here, and this means having a NPR stop in Bradford.
"We welcome the Transpennine Route Upgrade programme, but we’ve been clear that this should be as well as Northern Powerhouse Rail, not instead of it. By having the right transport infrastructure, I believe that there are no limits to what the city of Bradford could achieve."
Henri Murison, director of the Northern Powerhouse Partnership, said: “In the Prime Minister’s first major policy speech in Manchester, he committed to building Northern Powerhouse Rail across the Pennines.
"Rumours that this commitment will be broken are deeply concerning for Northern leaders who are working towards rebalancing the economy.
“The North was promised HS2 and Northern Powerhouse Rail in full - to be abandoned now, just as we begin a recovery from the pandemic, would be a hammer blow.
“We need reassurance and certainty that there is no substance to these rumours - which means an Integrated Rail Plan published before the summer recess.
“We need a new high-speed rail station built in Bradford city centre and we need to start construction on the Eastern Leg from Leeds in order to unlock connectivity benefits early. That includes getting more frequent and reliable services from the North East to Sheffield.”
But government sources insist no decision has yet been taken and that they will all be subject to the Integrated Rail Plan, which will set out how NPR, HS2 and TRU will fit together and is due to be published later this year. The Yorkshire Post understands options which could serve both Bradford and Huddersfield have been looked at.
A Government spokeswoman said: “The Integrated Rail Plan will soon outline exactly how major rail projects, including HS2 phase 2b, the Transpennine Route Upgrade and other transformational projects such as Northern Powerhouse Rail, will work together to deliver the reliable train services that passengers across the North and Midlands need and deserve.”
The leaked report seen by The Yorkshire Post says: "A long-term vision for the region has been developed by Northern Powerhouse Rail which comprises a blend of enhancements to existing routes and brand-new rail lines, notably a high speed line linking Manchester and Leeds.
"This would form a transformational new investment for the 2030s and beyond, building on HS2. The TRU programme is driven by the need to address the more immediate constraints to achieving the strategic objectives on the existing railway (solving today's problems)."
Tim Wood, Interim Chief Executive at Transport for the North, said: “Transport for the North welcomes any further potential investment by Government into the Transpennine Route Upgrade programme after its latest injection just a few weeks ago of £317m, the proposals provide a step change in capacity and resilience for both passengers and freight and moves us away from an ageing Victorian railway between Manchester and Leeds.
"Transport for the North and its Members have long been calling for full electrification of the route and major infrastructure upgrades which will drive our economy, jobs and place making.
"We now await the publication of the Integrated Rail Plan by Government due soon to transform connectivity across the North including great cities like Bradford which has been held back for far too long.”
Asked last week whether the Government was now more interested in smaller-scale transport infrastructure projects than big-ticket items like NPR, Chancellor Rishi Sunak told The Yorkshire Post: "I think we're doing both.
"The Prime Minister's said we are going to deliver an infrastructure revolution and that's what we're delivering. So it does mean big projects like HS2, but it also means those small scale infrastructure projects that are going to make a difference whether it's upgrading a station like Darlington, whether it's improving connectivity across the Pennines, whether it's the intra-city transport around cities like Leeds.
"In different cities, it will mean different things. It could be buses, it could be cycleways, it could be trams, but it's about connecting the cities within themselves. So I think we can, can do both and we are doing both, both are important for our future prosperity."
He added: "And with regard to the rest of the [Northern Powerhouse Rail] route, I'm a big believer in transport connectivity across the North as being something that's really important for us to deliver.
"We said later this year we'll publish something called the Integrated rail plan which will bring together all the various proposals for transport investment across the North and the Midlands and figure out what's the best package of all of those to do over what timeframe."